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CATaDa reveals global remodelling of chromatin accessibility during stem cell differentiation in vivo

During development eukaryotic gene expression is coordinated by dynamic changes in chromatin structure. Measurements of accessible chromatin are used extensively to identify genomic regulatory elements. Whilst chromatin landscapes of pluripotent stem cells are well characterised, chromatin accessibi...

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Detalles Bibliográficos
Autores principales: Aughey, Gabriel N, Estacio Gomez, Alicia, Thomson, Jamie, Yin, Hang, Southall, Tony D
Formato: Online Artículo Texto
Lenguaje:English
Publicado: eLife Sciences Publications, Ltd 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5826290/
https://www.ncbi.nlm.nih.gov/pubmed/29481322
http://dx.doi.org/10.7554/eLife.32341
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author Aughey, Gabriel N
Estacio Gomez, Alicia
Thomson, Jamie
Yin, Hang
Southall, Tony D
author_facet Aughey, Gabriel N
Estacio Gomez, Alicia
Thomson, Jamie
Yin, Hang
Southall, Tony D
author_sort Aughey, Gabriel N
collection PubMed
description During development eukaryotic gene expression is coordinated by dynamic changes in chromatin structure. Measurements of accessible chromatin are used extensively to identify genomic regulatory elements. Whilst chromatin landscapes of pluripotent stem cells are well characterised, chromatin accessibility changes in the development of somatic lineages are not well defined. Here we show that cell-specific chromatin accessibility data can be produced via ectopic expression of E. coli Dam methylase in vivo, without the requirement for cell-sorting (CATaDa). We have profiled chromatin accessibility in individual cell-types of Drosophila neural and midgut lineages. Functional cell-type-specific enhancers were identified, as well as novel motifs enriched at different stages of development. Finally, we show global changes in the accessibility of chromatin between stem-cells and their differentiated progeny. Our results demonstrate the dynamic nature of chromatin accessibility in somatic tissues during stem cell differentiation and provide a novel approach to understanding gene regulatory mechanisms underlying development.
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spelling pubmed-58262902018-02-28 CATaDa reveals global remodelling of chromatin accessibility during stem cell differentiation in vivo Aughey, Gabriel N Estacio Gomez, Alicia Thomson, Jamie Yin, Hang Southall, Tony D eLife Developmental Biology and Stem Cells During development eukaryotic gene expression is coordinated by dynamic changes in chromatin structure. Measurements of accessible chromatin are used extensively to identify genomic regulatory elements. Whilst chromatin landscapes of pluripotent stem cells are well characterised, chromatin accessibility changes in the development of somatic lineages are not well defined. Here we show that cell-specific chromatin accessibility data can be produced via ectopic expression of E. coli Dam methylase in vivo, without the requirement for cell-sorting (CATaDa). We have profiled chromatin accessibility in individual cell-types of Drosophila neural and midgut lineages. Functional cell-type-specific enhancers were identified, as well as novel motifs enriched at different stages of development. Finally, we show global changes in the accessibility of chromatin between stem-cells and their differentiated progeny. Our results demonstrate the dynamic nature of chromatin accessibility in somatic tissues during stem cell differentiation and provide a novel approach to understanding gene regulatory mechanisms underlying development. eLife Sciences Publications, Ltd 2018-02-26 /pmc/articles/PMC5826290/ /pubmed/29481322 http://dx.doi.org/10.7554/eLife.32341 Text en © 2018, Aughey et al http://creativecommons.org/licenses/by/4.0/ http://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited.
spellingShingle Developmental Biology and Stem Cells
Aughey, Gabriel N
Estacio Gomez, Alicia
Thomson, Jamie
Yin, Hang
Southall, Tony D
CATaDa reveals global remodelling of chromatin accessibility during stem cell differentiation in vivo
title CATaDa reveals global remodelling of chromatin accessibility during stem cell differentiation in vivo
title_full CATaDa reveals global remodelling of chromatin accessibility during stem cell differentiation in vivo
title_fullStr CATaDa reveals global remodelling of chromatin accessibility during stem cell differentiation in vivo
title_full_unstemmed CATaDa reveals global remodelling of chromatin accessibility during stem cell differentiation in vivo
title_short CATaDa reveals global remodelling of chromatin accessibility during stem cell differentiation in vivo
title_sort catada reveals global remodelling of chromatin accessibility during stem cell differentiation in vivo
topic Developmental Biology and Stem Cells
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5826290/
https://www.ncbi.nlm.nih.gov/pubmed/29481322
http://dx.doi.org/10.7554/eLife.32341
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